added check to cluster.classic to make sure file type is phylip. added mapping funct...

[mothur.git] / otuassociationcommand.cpp

diff --git a/otuassociationcommand.cpp b/otuassociationcommand.cpp
index 4b5596441081ce9e2becf9df5d61c4f4636a51e3..0d41e63f3526bc9af4e3933d5f3337d62ebd0f2a 100644 (file)
--- a/otuassociationcommand.cpp
+++ b/otuassociationcommand.cpp
@@ -300,18 +300,6 @@ int OTUAssociationCommand::process(vector<SharedRAbundVector*>& lookup){
                        for (int k = 0; k < i; k++) {
                                
                                if (m->control_pressed) { out.close(); return 0; }
-                               
-                /*cout << m->binLabelsInFile[i] << " <- c(" << xy[i][0];
-                for (int l = 1; l < xy[i].size(); l++){
-                    cout << ", " << xy[i][l];
-                }
-                cout << ")\n";
-                
-                cout << m->binLabelsInFile[k] << " <- c(" << xy[k][0];
-                for (int l = 1; l < xy[k].size(); l++){
-                    cout << ", " << xy[k][l];
-                }
-                cout << ")\n";*/
 
                                double coef = 0.0;
                                double sig = 0.0;
@@ -320,7 +308,7 @@ int OTUAssociationCommand::process(vector<SharedRAbundVector*>& lookup){
                                else if (method == "kendall")   {       coef = linear.calcKendall(xy[i], xy[k], sig);   }                   
                                else { m->mothurOut("[ERROR]: invalid method, choices are spearman, pearson or kendall."); m->mothurOutEndLine(); m->control_pressed = true; }
                        
-                               out << m->binLabelsInFile[i] << '\t' << m->binLabelsInFile[k] << '\t' << coef << '\t' << sig << endl;
+                out << m->binLabelsInFile[i] << '\t' << m->binLabelsInFile[k] << '\t' << coef << '\t' << sig << endl;
                        }
                }
                
@@ -448,7 +436,7 @@ int OTUAssociationCommand::process(vector<SharedRAbundFloatVector*>& lookup){
                                else if (method == "kendall")   {       coef = linear.calcKendall(xy[i], xy[k], sig);   }                   
                                else { m->mothurOut("[ERROR]: invalid method, choices are spearman, pearson or kendall."); m->mothurOutEndLine(); m->control_pressed = true; }
                                
-                               out << m->binLabelsInFile[i] << '\t' << m->binLabelsInFile[k] << coef << '\t' << sig << endl;
+                out << m->binLabelsInFile[i] << '\t' << m->binLabelsInFile[k] << '\t' << coef << '\t' << sig << endl; 
                        }
                }